Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example?
As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map. I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file). Thanks, Eileen. > ------------------------------ > > Message: 10 > Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) > From: Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <alpine.lrh.2.03.1407170411110.12...@nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Eileen - All image formats that mri_convert (and thus any freesurfer > program) can read will do, you don't need dicom. Try giving trac-all the > phase difference maps you have and let's see what happens. > > Best, > a.y > > On Wed, 16 Jul 2014, Eileen Moore wrote: > > > Hi Anastasia, > > > > OK - our imaging physicists had developed a wrapper script around > epidewarp > > which takes our dicom images and converts them into the phase difference > map > > (it is based on the script that was authored by Doug Greve for the fBIRN > > consortium). It looks like the tracula script requires dicom images. Is > > there a way for me to do epidewarp manually and then follow through with > the > > remaining steps using trac-all? > > > > Thanks, > > Eileen. > > > > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > > From: Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > Message-ID: > > <alpine.lrh.2.03.1407141119560.23...@nmr.mgh.harvard.edu> > > Content-Type: text/plain; charset="utf-8" > > > > > > Hi Eileen - That step is run with the program epidewarp.fsl, > > which you can > > run on the command line to see the available options. The input > > phase map > > volume is expected to have either 2 frames (2 separate phase > > maps) or 1 > > frame (the difference phase map). This error from trac-all means > > that it > > found that your input phase map has something other than 1 or 2 > > frames, so > > it doesn't know how to handle it. > > > > Hope this helps, > > a.y > > > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > > I'm tyring to > > > run tracula on some? images acquired from a GE scanner. I am > > running into > > > problems when I try to perform the registration-based > > B0-inhomogeneity > > > compensation, getting an error in the terminal output: "ERROR: > > Unrecognized > > > format of phase map". However, trac-all -prep runs fine when I > > skip the > > > B0-inhomogeneity compensation step. Is there something else I > > need to do to > > > use field map correction? > > > > > > I've attached the trac-all.log and a copy of the terminal > > output. > > > > > > Thanks, > > > Eileen. > > > > > > > > > > > > > > > > > > > >
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/image/FASD/Shared/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl brain:~> cd freesurfer/ brain:~/freesurfer> ls DICOM_FILES FreeSurfer_Scripts sessions subjects tracula brain:~/freesurfer> cd tracula brain:~/freesurfer/tracula> ls CIFASD2-DTI-pilot CIFASDII_T1-DTI dmrirc.example DTI-30 DTI-30_pilot error.log brain:~/freesurfer/tracula> cd CIFASDII_T1-DTI/ brain:~/freesurfer/tracula/CIFASDII_T1-DTI> ls bvals call1285_CIFASDII_T1_021210 dmrirc.CIFASDII_T1-DTI~ terminal-output-error.txt bvecs dmrirc.CIFASDII_T1-DTI dmrirc.file brain:~/freesurfer/tracula/CIFASDII_T1-DTI> gedit dmri dmrirc.CIFASDII_T1-DTI~ dmrirc.CIFASDII_T1-DTI dmrirc.file brain:~/freesurfer/tracula/CIFASDII_T1-DTI> gedit dmrirc.* brain:~/freesurfer/tracula/CIFASDII_T1-DTI> trac-all -prep -c ERROR: flag -c requires one argument brain:~/freesurfer/tracula/CIFASDII_T1-DTI> pwd /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI brain:~/freesurfer/tracula/CIFASDII_T1-DTI> trac-all -prep -c /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/dm dmrirc.CIFASDII_T1-DTI~ dmrirc.CIFASDII_T1-DTI dmrirc.file brain:~/freesurfer/tracula/CIFASDII_T1-DTI> trac-all -prep -c /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/dmrirc.CIFASDII dmrirc.CIFASDII_T1-DTI~ dmrirc.CIFASDII_T1-DTI brain:~/freesurfer/tracula/CIFASDII_T1-DTI> trac-all -prep -c /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/dmrirc.CIFASDII_T1-DTI INFO: SUBJECTS_DIR is /home/image/FASD/Shared/freesurfer/subjects/CIFASDII_T1 INFO: Diffusion root is /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI Actual FREESURFER_HOME /usr/local/freesurfer trac-preproc -c /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/scripts/dmrirc.local -log /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/scripts/trac-all.log -cmd /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Aug 27 12:44:49 PDT 2014 mri_convert /home/image/FASD/call1285/call1285_dti_021210/raw/s3851205/i00001.CFMRI.1 /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig.nii.gz mri_convert /home/image/FASD/call1285/call1285_dti_021210/raw/s3851205/i00001.CFMRI.1 /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/image/FASD/call1285/call1285_dti_021210/raw/s3851205/i00001.CFMRI.1... Starting DICOMRead2() dcmfile = /home/image/FASD/call1285/call1285_dti_021210/raw/s3851205/i00001.CFMRI.1 dcmdir = /home/image/FASD/call1285/call1285_dti_021210/raw/s3851205 Ref Series No = 8 Found 1149 files, checking for dicoms Found 1147 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 3 Vs: 0 0 1 Second Sorting Counting frames nframes = 31 nslices = 37 ndcmfiles = 1147 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=13000.00, TE=98.50, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig.nii.gz... mri_probedicom --i /home/image/FASD/call1285/call1285_dti_021210/raw/s3851205/i00001.CFMRI.1 > /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dcminfo.dat cp /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/bvecs /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig.mghdti.bvecs cp /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/bvals /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig.mghdti.bvals flip4fsl /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig.nii.gz /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 10.5469 fslswapdim /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig.nii.gz x -y z /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig_flip.nii.gz INFO: found /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig_flip.mghdti.bvecs /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/bvecs mv -f /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig_flip.mghdti.bvals /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/bvals eddy_correct /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_orig_flip.nii.gz /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi.nii.gz 0 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0000 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0001 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0002 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0003 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0004 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0005 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0006 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0007 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0008 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0009 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0010 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0011 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0012 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0013 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0014 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0015 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0016 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0017 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0018 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0019 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0020 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0021 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0022 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0023 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0024 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0025 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0026 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0027 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0028 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0029 processing /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_tmp0030 mv -f /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/bvecs /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/bvecs.norot xfmrot /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi.ecclog /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/bvecs.norot /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/bvecs mv -f /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi.nii.gz /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/dwi_eddy.nii.gz mri_convert /home/image/FASD/call1285/call1285_dti_021210/proc/mag_te1_rs.nii.gz /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0mag.nii.gz mri_convert /home/image/FASD/call1285/call1285_dti_021210/proc/mag_te1_rs.nii.gz /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0mag.nii.gz niiRead(): error opening file /home/image/FASD/call1285/call1285_dti_021210/proc/mag_te1_rs.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/image/FASD/call1285/call1285_dti_021210/proc/mag_te1_rs.nii.gz... flip4fsl /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0mag.nii.gz /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0mag.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -10.5469 fslswapdim /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0mag.nii.gz x y z /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0mag.nii.gz fslorient -forceradiological /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0mag.nii.gz mri_convert /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0pha.nii.gz mri_convert /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0pha.nii.gz niiRead(): unsupported datatype 32 (with scl_slope != 0) in /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii... flip4fsl /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0pha.nii.gz /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0pha.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -10.5469 fslswapdim /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0pha.nii.gz x y z /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0pha.nii.gz fslorient -forceradiological /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0pha.nii.gz mri_probedicom --i /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii > /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII_T1_021210/dmri/b0info.dat Linux brain 3.2.0-61-generic #93-Ubuntu SMP Fri May 2 21:31:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Aug 27 12:49:17 PDT 2014 brain:~/freesurfer/tracula/CIFASDII_T1-DTI>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
